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X-WR-CALDESC:Events for Department of Theoretical Physics
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TZID:Europe/Ljubljana
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DTSTART:20220327T010000
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DTSTART;TZID=Europe/Ljubljana:20220301T130000
DTEND;TZID=Europe/Ljubljana:20220301T140000
DTSTAMP:20260427T141107
CREATED:20211203T175329Z
LAST-MODIFIED:20220223T094306Z
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SUMMARY:[Biophysics seminar] Gregor Posnjak: "From DNA origami to photonic crystals"
DESCRIPTION:The idea of using the predictable base pairing of DNA nucleobases for programmable assembly on the nanoscale dates back to the 1980s when the recently deceased Ned Seeman had the idea of using it to crystalize proteins on a DNA-based lattice for their structure determination with x-ray crystallography. After the first successful DNA nanostructures in the 1990s\, the real boom came after 2006 when the concept of DNA origami was introduced. The use of a long DNA scaffold strand in combination with short staple strands eliminated many of the short-comings of the earlier approaches and enabled robust programmable assembly with resolution on the order of nanometers. \nIn the first part of the talk I will introduce the concept of DNA origami and give a short review of the various structures and super-structures that were developed and their applications in drug delivery\, biophysics\, super-resolution microscopy\, sensing and plasmonics. In the second part I will shortly introduce photonic crystals as motivation for my work and then present a DNA-origami based self-assembled diamond lattice\, which we will use as a template for realization of visible spectrum photonic crystals.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-gregor-posnjak-dna-origami/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220308T130000
DTEND;TZID=Europe/Ljubljana:20220308T140000
DTSTAMP:20260427T141107
CREATED:20220119T113425Z
LAST-MODIFIED:20220119T113425Z
UID:5019-1646744400-1646748000@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Horacio Guzman: "Polymer swelling model based on dynamic AFM experiments"
DESCRIPTION:
URL:https://web-f1.ijs.si/event/biophysics-seminar-horacio-guzman-polymer-swelling-afm/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220317T150000
DTEND;TZID=Europe/Ljubljana:20220317T160000
DTSTAMP:20260427T141107
CREATED:20220311T162205Z
LAST-MODIFIED:20220311T162252Z
UID:5056-1647529200-1647532800@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Mauricio Comas-García: "Understanding selective packaging in Alphaviruses"
DESCRIPTION:Alphaviruses are a genus of positive-sense single-stranded RNA viruses that infect mammals and are transmitted by mosquitos. These viruses can cause a wide range of diseases\, from dengue-like symptoms (e.g.\, Chikungunya virus) to encephalitis (e.g.\, Venezuelan Equine Encephalitis virus). While during the ’80 and ’90s\, there was a great deal of interest in studying these viruses\, with time\, other pathogens became more attractive for research purposes. However\, the spread of the Chikungunya virus during the beginning of the XXI century to Asia\, Oceania\, and the Americas has brought new attention to these viruses. \nThese viruses have been widely studied from several aspects; structural biology\, epidemiology\, and immunology. For example\, we know the 3D structure of most of these viruses with almost an atomic detail. Furthermore\, a series of in vitro assembly experiments have shed light on some of the key RNA-protein interactions that are needed for core-like-practice assembly. Nonetheless\, there is very little information on how these viruses select their genome during infection. \nOur group has been working on creating a series of plasmids for expression in mammalian cells that contain a series of viral elements from the Chikungunya virus. The goal of these constructs is to generate a system that allows us to carry out competition experiments between mutant and wild-type viral RNAs in infected cells to find the packaging signal in the genomic RNAs that allows for its selective packaging. In this seminar\, we will present some preliminary results and the strategy we are following to understand how RNA structure and sequence determine selective packaging in an infected cell.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-mauricio-comas-garcia-selective-packaging-alphaviruses/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220324T130000
DTEND;TZID=Europe/Ljubljana:20220324T140000
DTSTAMP:20260427T141107
CREATED:20220308T094513Z
LAST-MODIFIED:20220319T195149Z
UID:5054-1648126800-1648130400@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Simon Čopar: "Hyperuniformity and spherical structure factor"
DESCRIPTION:Hyperuniformity is an interesting measure of order which detects and quantifies long range positional correlations without requiring local crystalline order. This measure can be defined in real space\, through scaling of fluctuations of the number of building blocks in asymptotically large volumes\, or in frequency space\, where hyperuniformity manifests as a gap in the structure factor. \nI will review the hyperuniformity concepts and highlight the main obstacles and solutions that arise when dealing with a spherical geometry. I will present it on a few model spherical lattices.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-simon-copar-hyperuniformity/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220329T130000
DTEND;TZID=Europe/Ljubljana:20220329T140000
DTSTAMP:20260427T141107
CREATED:20220316T090207Z
LAST-MODIFIED:20220318T110115Z
UID:5061-1648558800-1648562400@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Aljaž Godec: "From the kinetic Ising model to specific cell adhesion\, and back"
DESCRIPTION:By exploiting a mapping onto a kinetic Ising-like model we will illuminate the many-body effects underlying the structure\, formation\, and dissolution of cellular adhesion domains in the presence and absence of external forces. We will present analytical results on the pair-correlation level for the complete thermodynamics and kinetics of adhesion clusters of any size\, including the thermodynamic limit. A new kind of dynamical phase transition will be demonstrated: the mean formation and dissolution times per adhesion bond change discontinuously with respect to the bond-coupling parameter that in turn is controlled by the membrane rigidity. At the dynamical critical point\, adhesion cluster formation and dissolution are the fastest\, while the statistically dominant transition path undergoes a qualitative change. In the context of the classical Ising model the dynamical phase transition reflects a first order discontinuity in the magnetization-reversal time. Will will conclude by briefly discussing the relevance of these results for the mechanical regulation of cell adhesion\, and argue that it is biologically favorable if cell adhesion is poised at criticality.  \n[1] K. Blom & A. Godec\, Phys. Rev. X 11\, 031067 (2021).\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-aljaz-godec-kinetic-ising-cell-adhesion/
LOCATION:Zoom
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